User:Wayne Decatur/Sandbox Glutamate receptor: Difference between revisions
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kg2 OCA], [http://www.ebi.ac.uk/pdbsum/3kg2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3kg2 RCSB]</span> | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kg2 OCA], [http://www.ebi.ac.uk/pdbsum/3kg2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3kg2 RCSB]</span> | ||
}} | }} | ||
*Unanticipated is the domain swapping and crossover that occurs between the subunits interactions. In order to discuss the remarkable swapping, it is best to <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/ | *Unanticipated is the domain swapping and crossover that occurs between the subunits interactions. In order to discuss the remarkable swapping, it is best to <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/4'>designate each subunit with a letter</scene>: <br> '''<span style="color:forestgreen">A</span>''' '''<span style="color:red">B</span>''' '''<span style="color:cornflowerblue">C</span>''' '''<!--<span style="color:#FFFF80">D</span>-->D''' | ||
*Considering each chain, there is crossover as the pairs of subunits seen in the ATD are swapped in the LBD. | *Considering each chain, there is crossover as the pairs of subunits seen in the ATD are swapped in the LBD. | ||
::In the ATD domain - | ::In the ATD domain - | ||
::*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ab_in_atd/1'>Portions of the A and B subunits pair up</scene>. | ::*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ab_in_atd/1'>Portions of the A and B subunits pair up</scene>. | ||
::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Cd_in_atd/ | ::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Cd_in_atd/2'>Portions of the C and D subunits form a pair</scene>. | ||
::*While that is going on, in the ATD there is also inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_atd/ | ::*While that is going on, in the ATD there is also inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_atd/2'>subunits B and D</scene>. Note this view really highlights the two-fold symmetry between the A-B and C-D pairs at the level of the ATD. | ||
::In the LBD domain - | ::In the LBD domain - | ||
::*Whereas in the ATD domain A and B paired up, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ad_in_lbd/ | ::*Whereas in the ATD domain A and B paired up, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ad_in_lbd/3'>portions of the A and D subunits pair up</scene> in the LBD. | ||
::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bc_in_lbd/1'>Portions of the B and C subunits form a pair</scene>. | ::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bc_in_lbd/1'>Portions of the B and C subunits form a pair</scene>. | ||
::*While that is going on, in the LBD there is also extensive inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbd/6'>subunits A and C</scene>. Note this view highlights the two-fold symmetry between the A-D and B-C pairs at the level of the LBD. <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbdside/1'>Looking from the side helps in seeing the inter-pair interactions between A and C</scene>. | ::*While that is going on, in the LBD there is also extensive inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbd/6'>subunits A and C</scene>. Note this view highlights the two-fold symmetry between the A-D and B-C pairs at the level of the LBD. <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbdside/1'>Looking from the side helps in seeing the inter-pair interactions between A and C</scene>. | ||
:The domain swapping can be observed from the side following the backbone of each chain as well: <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/1'>A chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/2'>B chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/3'>C chain</scene>, and <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/ | :The domain swapping can be observed from the side following the backbone of each chain as well: <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/1'>A chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/2'>B chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/3'>C chain</scene>, and <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/5'>D chain</scene>. And <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/4'>all for comparison</scene>. | ||
*As explored further in [[#Transmembrane domain architecture and the occluded pore|a later section below]] , the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmd_domain_4fold/2'>symmetry is an overall four-fold for the TMD</scene> and thus remarkably the symmetry switches from an overall two-fold symmetry for the ATD and LBD to four-fold for the TMD. | *As explored further in [[#Transmembrane domain architecture and the occluded pore|a later section below]] , the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmd_domain_4fold/2'>symmetry is an overall four-fold for the TMD</scene> and thus remarkably the symmetry switches from an overall two-fold symmetry for the ATD and LBD to four-fold for the TMD. | ||
